strip_sequence {PepMapViz} | R Documentation |
Strip peptide sequences based on the specified data type
Description
This function takes outputs from multiple platform, a data frame with a column containing peptide sequences to be stripped, and a column where the stripped sequences will be stored. The function chooses the appropriate stripping method based on the specified data type ('PEAKS', 'Spectronaut', 'MSFragger', 'Comet', 'DIANN', 'Skyline' or 'Maxquant').
Usage
strip_sequence(data, column, convert_column, type)
Arguments
data |
A data frame with the peptide sequences. |
column |
The name of the column containing the peptide sequences to be stripped. |
convert_column |
The name of the column where the stripped sequences will be stored. |
type |
A character string specifying the data type (e.g. 'Skyline' or 'Maxquant'). |
Value
A data frame with the specified column containing stripped sequences.
Examples
library(data.table)
data_skyline <- data.table(
'Peptide Modified Sequence' = c(
"AGLC[+57]QTFVYGGC[+57]R",
"AAAASAAEAGIATTGTEDSDDALLK",
"IVGGWEC[+57]EK"
),
Condition = c("A", "B", "B")
)
data_maxquant <- data.table(
'Modified sequence' = c(
"_(ac)AAAAELRLLEK_",
"_EAAENSLVAYK_",
"_AADTIGYPVM(ox)IRSAYALGGLGSGICPNK_"
),
Condition = c("A", "B", "B")
)
converted_data_skyline <- strip_sequence(data_skyline,
'Peptide Modified Sequence',
'Sequence',
"Skyline")
converted_data_maxquant <- strip_sequence(data_maxquant, 'Modified sequence',
'Sequence', "Maxquant")
[Package PepMapViz version 1.1.0 Index]